R Notebook

library(Seurat)

## Loading required package: ggplot2

## Loading required package: cowplot

## 
## Attaching package: 'cowplot'

## The following object is masked from 'package:ggplot2':
## 
##     ggsave

## Loading required package: Matrix

seurobj <- readRDS('/projects/pytrik/sc_adipose/analyze_10x_fluidigm/data/10x-180831')

VlnPlot(seurobj, c("nGene", "percent.mito", "nUMI"), group.by='timepoint', nCol = 1, point.size.use=-1)

GenePlot(seurobj, 'nUMI', 'nGene', cex.use = 0.5)

PCElbowPlot(seurobj) #15 pcs?

PCAPlot(seurobj, group.by='timepoint', pt.size=0.1)

TSNEPlot(seurobj, group.by='timepoint', pt.size=0.1)

TSNEPlot(seurobj, group.by='Phase', pt.size=0.1)

FeaturePlot(seurobj, features.plot = 'nUMI', cols.use=c('grey', 'blue'), no.legend=F)

FeaturePlot(seurobj, features.plot = 'percent.mito', cols.use=c('grey', 'blue'), no.legend = F)

FeaturePlot(seurobj, features.plot = 'nGene', cols.use=c('grey', 'blue'), no.legend = F)

FeaturePlot(seurobj, features.plot = 'EBF2', cols.use=c('grey', 'blue'), no.legend = F)

FeaturePlot(seurobj, features.plot = 'TM4SF1', cols.use=c('grey', 'blue'), no.legend = F)

FeaturePlot(seurobj, features.plot = 'LY6K', cols.use=c('grey', 'blue'), no.legend = F)

FeaturePlot(seurobj, features.plot = 'PDGFRA', cols.use=c('grey', 'blue'), no.legend = F)

TSNEPlot(seurobj, group.by='res.0.5', pt.size=0.1)

TSNEPlot(seurobj, group.by='timepoint', pt.size=0.1)